From: SourceForge.net <no...@so...> - 2008-10-23 12:59:30
|
Bugs item #2189340, was opened at 2008-10-23 14:44 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2189340&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Jonathan Alvarsson (jonalv) Assigned to: Nobody/Anonymous (nobody) Summary: Resource trouble in OSGI environment (Bioclipse) Initial Comment: We (Bioclipse) have had some trouble loading related to jmol resource loading, in particular related to the "minimize" commando. Some trials has resulted in a patch that makes things work for us. Sadly I can not be too exact on why it works though. All it does is that it reads the resource as a stream at once instead of creating a url for the resource and then a stream from that url. Presumably there has been some trouble with reading that url since we have gotten a java.net.UnknownServiceException at the url.getContent() call. So if there is no vital reason to take the detour trough a url I suggest the change described in attached patch. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2189340&group_id=23629 |
From: SourceForge.net <no...@so...> - 2008-10-23 13:26:52
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Bugs item #2189340, was opened at 2008-10-23 14:44 Message generated for change (Comment added) made by jonalv You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2189340&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Jonathan Alvarsson (jonalv) Assigned to: Nobody/Anonymous (nobody) Summary: Resource trouble in OSGI environment (Bioclipse) Initial Comment: We (Bioclipse) have had some trouble loading related to jmol resource loading, in particular related to the "minimize" commando. Some trials has resulted in a patch that makes things work for us. Sadly I can not be too exact on why it works though. All it does is that it reads the resource as a stream at once instead of creating a url for the resource and then a stream from that url. Presumably there has been some trouble with reading that url since we have gotten a java.net.UnknownServiceException at the url.getContent() call. So if there is no vital reason to take the detour trough a url I suggest the change described in attached patch. ---------------------------------------------------------------------- >Comment By: Jonathan Alvarsson (jonalv) Date: 2008-10-23 15:26 Message: Yes, it seems that changing name from UFF.prm to UFF.txt as suggested by ha...@st... also fixes the problem. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2189340&group_id=23629 |
From: SourceForge.net <no...@so...> - 2008-11-01 18:29:09
|
Bugs item #2189340, was opened at 2008-10-23 14:44 Message generated for change (Comment added) made by egonw You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2189340&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Jonathan Alvarsson (jonalv) Assigned to: Nobody/Anonymous (nobody) Summary: Resource trouble in OSGI environment (Bioclipse) Initial Comment: We (Bioclipse) have had some trouble loading related to jmol resource loading, in particular related to the "minimize" commando. Some trials has resulted in a patch that makes things work for us. Sadly I can not be too exact on why it works though. All it does is that it reads the resource as a stream at once instead of creating a url for the resource and then a stream from that url. Presumably there has been some trouble with reading that url since we have gotten a java.net.UnknownServiceException at the url.getContent() call. So if there is no vital reason to take the detour trough a url I suggest the change described in attached patch. ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2008-11-01 19:29 Message: The renaming to .txt worked. Maybe this can be applied to Jmol 11.6.x? ---------------------------------------------------------------------- Comment By: Jonathan Alvarsson (jonalv) Date: 2008-10-23 15:26 Message: Yes, it seems that changing name from UFF.prm to UFF.txt as suggested by ha...@st... also fixes the problem. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2189340&group_id=23629 |
From: SourceForge.net <no...@so...> - 2008-11-01 22:22:58
|
Bugs item #2189340, was opened at 2008-10-23 07:44 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2189340&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Jonathan Alvarsson (jonalv) >Assigned to: Bob Hanson (hansonr) Summary: Resource trouble in OSGI environment (Bioclipse) Initial Comment: We (Bioclipse) have had some trouble loading related to jmol resource loading, in particular related to the "minimize" commando. Some trials has resulted in a patch that makes things work for us. Sadly I can not be too exact on why it works though. All it does is that it reads the resource as a stream at once instead of creating a url for the resource and then a stream from that url. Presumably there has been some trouble with reading that url since we have gotten a java.net.UnknownServiceException at the url.getContent() call. So if there is no vital reason to take the detour trough a url I suggest the change described in attached patch. ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2008-11-01 17:22 Message: 11.6.2/11.7.7 have UFF.txt ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2008-11-01 13:29 Message: The renaming to .txt worked. Maybe this can be applied to Jmol 11.6.x? ---------------------------------------------------------------------- Comment By: Jonathan Alvarsson (jonalv) Date: 2008-10-23 08:26 Message: Yes, it seems that changing name from UFF.prm to UFF.txt as suggested by ha...@st... also fixes the problem. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2189340&group_id=23629 |
From: Robert H. <ha...@st...> - 2008-10-23 13:09:15
|
Before doing that, could you please try again with the original code, but rename the resource UFF.txt ? I'd like to know if the problem is that the .prm is sending some odd MIME type to Url.getContent() Bob On Thu, Oct 23, 2008 at 7:44 AM, SourceForge.net <no...@so...>wrote: > Bugs item #2189340, was opened at 2008-10-23 14:44 > Message generated for change (Tracker Item Submitted) made by Item > Submitter > You can respond by visiting: > > https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2189340&group_id=23629 > > Please note that this message will contain a full copy of the comment > thread, > including the initial issue submission, for this request, > not just the latest update. > Category: None > Group: None > Status: Open > Resolution: None > Priority: 5 > Private: No > Submitted By: Jonathan Alvarsson (jonalv) > Assigned to: Nobody/Anonymous (nobody) > Summary: Resource trouble in OSGI environment (Bioclipse) > > Initial Comment: > We (Bioclipse) have had some trouble loading related to jmol resource > loading, in particular related to the "minimize" commando. Some trials has > resulted in a patch that makes things work for us. Sadly I can not be too > exact on why it works though. All it does is that it reads the resource as a > stream at once instead of creating a url for the resource and then a stream > from that url. > > Presumably there has been some trouble with reading that url since we have > gotten a java.net.UnknownServiceException at the url.getContent() call. > > So if there is no vital reason to take the detour trough a url I suggest > the change described in attached patch. > > ---------------------------------------------------------------------- > > You can respond by visiting: > > https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2189340&group_id=23629 > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Robert H. <ha...@st...> - 2008-10-23 13:12:02
|
(two places that's referred to in ForceFieldUFF.java) On Thu, Oct 23, 2008 at 8:08 AM, Robert Hanson <ha...@st...> wrote: > Before doing that, could you please try again with the original code, but > rename the resource > > UFF.txt > > ? > > I'd like to know if the problem is that the .prm is sending some odd MIME > type to Url.getContent() > > Bob > > > > On Thu, Oct 23, 2008 at 7:44 AM, SourceForge.net <no...@so...>wrote: > >> Bugs item #2189340, was opened at 2008-10-23 14:44 >> Message generated for change (Tracker Item Submitted) made by Item >> Submitter >> You can respond by visiting: >> >> https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2189340&group_id=23629 >> >> Please note that this message will contain a full copy of the comment >> thread, >> including the initial issue submission, for this request, >> not just the latest update. >> Category: None >> Group: None >> Status: Open >> Resolution: None >> Priority: 5 >> Private: No >> Submitted By: Jonathan Alvarsson (jonalv) >> Assigned to: Nobody/Anonymous (nobody) >> Summary: Resource trouble in OSGI environment (Bioclipse) >> >> Initial Comment: >> We (Bioclipse) have had some trouble loading related to jmol resource >> loading, in particular related to the "minimize" commando. Some trials has >> resulted in a patch that makes things work for us. Sadly I can not be too >> exact on why it works though. All it does is that it reads the resource as a >> stream at once instead of creating a url for the resource and then a stream >> from that url. >> >> Presumably there has been some trouble with reading that url since we have >> gotten a java.net.UnknownServiceException at the url.getContent() call. >> >> So if there is no vital reason to take the detour trough a url I suggest >> the change described in attached patch. >> >> ---------------------------------------------------------------------- >> >> You can respond by visiting: >> >> https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2189340&group_id=23629 >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win great >> prizes >> Grand prize is a trip for two to an Open Source event anywhere in the >> world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |